mcxarray can either read a flat file containing array data (-data)
or a matrix file satisfying the mcl input format (-imx). In the
former case it will by default work with the rows as the data vectors. In
the latter case it will by default work with the columns as the data
vectors (note that mcl matrices are presented as a listing of columns).
This can be changed for both using the
--transpose option.

The input data may contain missing data in the form of empty columns,
NA values (not available/applicable), or NaN values (not a number).
The program keeps track of these, and when computing the correlation
between two rows or columns ignores all positions where any one of
the two has missing data.

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-l <num> (take labels from column <num>)
Specifies to construct a tab of labels from this data column.
The tab can be written to file using -write-tabfname.

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-write-tab <fname> (write row labels to file)
Write a tab file. In the simple case where the labels are in the first
data column it is sufficient to issue -skipc1.
If more data columns need to be skipped one must explicitly specify
the data column to take labels from with -ll.

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-t <int> (use <int> threads)
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-J <intJ> (a total of <intJ> jobs are used)
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-j <intj> (this job has index <intj>)
Computing all pairwise correlations is time-intensive for large input.
If you have multiple CPUs available consider using
as many threads. Additionally it is possible to
spread the computation over multiple jobs/machines.
Conceptually, each job takes a number of threads from
the total thread pool.
Additionally, the number of threads (as specified by -t)
currently must be the same for all jobs, as it is used
by each job to infer its own set of tasks.
The following set of options, if given to as many commands,
defines three jobs, each running four threads.

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--job-info (print index ranges for this job)
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-start <int> (start at column <int> inclusive)
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-end <int> (end at column <int> EXclusive)
--job-info can be used to list the set of column
ranges to be processed by the job as a result of the command
line options -t, -J, and -j.
If a job has failed, this option can be used to manually
split those ranges into finer chunks, each to be processed
as a new sub-job specified with -start and -end.
With the latter two options, it is impossible to use
parallelization of any kind
(i.e. any of the -t, -J, and -j options).

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--transpose (work with the transpose)
Work with the transpose of the input data matrix.

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-write-data <fname> (write data to file)
This writes the data that was read in to file.
If --spearman is specified the data will
be rank-transformed.

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-write-na <fname> (write NA matrix to file)
This writes all positions for which no data was found
to file, in native mcl matrix format.

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--zero-as-na (treat zeroes as missing data)
This option can be useful when reading data with the -imx option,
for example after it has been loaded from label input by mcxload.
An example case is the processing of a large number of probe rankings,
where not all rankings contain all probe names. The rankings can be loaded
using mcxload with a tab file containing all probe names.
Probes that are present in the ranking are given a positive ordinal
number reflecting the ranking, and probes that are absent are implicitly
given the value zero. With the present option mcxarray will handle
the correlation computation in a reasonable way.

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--cosine (use cosine)
Use the cosine as correlation measure.

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-n mode (normalization mode)
If mode is set to z the data will be normalized
based on z-score. No other modes are currently supported.